We propose a series of simulations that will take advantage of recently determined structures for Eco RI and Eco RV endonucleases as well as our recently completed preliminary simulation of the DNA-Eco RI complex. Our preliminary simulation of the cognate DNA-Eco RI endonuclease complex employed a 6 A shell of explicit water for a total of approximately 15,000 atoms. We used AMBER 4.0 to simulate the complex for 170 pS and are currently analyzing the trajectory. The specific aims are: (1) extend the preliminary simulation of the native complex from its current curation of 170 pS to a final duration of 500 pS; (2) simulate the apo-protein (in the absence of DNA) for 250 pS using a similar protocol; (3) simulate the cognate DNA-Eco RV complex (4RVE) for 250 pS.